Like JohnS said, it is highly discouraged to run fsck on a mounted filesystem; there's enough risk in it performing changes on the filesystem that many tools outright prohibit you from conducting any operations on a mounted system. Changes occur rapidly on modern filesystems in use and the filesystem journal isn't constantly synced. This means that fsck almost certainly *will* find discrepancies and attempt to fix them. This is normal behavior for the tool and is something to be cautious about.

The only way (as far as I know) to run fsck properly is to do so on an unmounted filesystem. This way you can trust its output and make corrections if need be in order to have a clean filesystem. There aren't really any software configurations involved for your target filesystem. It's a standard procedure to boot into a separate root filesystem (such as a micro SD card if you are running on the NAND flash). It's annoying to do this, we understand, but the last thing we want to do is give you advice/recommendations that could potentially cause you data loss.

Can you run fsck again on the NAND flash storage device after booting with a micro SD and post the output?